You may need to set up a delay for the device. When I set mine up and the TV didn't change inputs properly I did it through the web interface. I could only select a 2 second delay though. Some devices when they turn on, they take a few seconds before you can set the input. That is probably the problem. One other possible issue is the input button didn't program automatically and may need to be "learned". If that doesn't work. I suggest adding a second input button on the remote, either a button or on the LCD, then when everything is on, just push it to get it to the right input. I have to do that with my projector because it takes 10 seconds to come on, much longer than the delay that can be set.
By the way, I'm starting to begin writing simple product reviews of A/V equipment I buy and own on my new site with remote control information http://thecreativealternative.com/logitech-harmony-650-remote/
I hope to get input from people as I progress with it and other products. When I was searching for information before buying the 650 I couldn't find a site easily with the information I needed so I decided to create one myself.